Comparative genomics has revealed that eukaryotic genomes harbor many orphan genes-- genes restricted to particular evolutionary lineages. Some of these are new genes with novel organizations and functions. How these new genes originate and become established is an important but poorly understood phenomenon shaping genome evolution. The aim of this project is to use whole genome sequences from 12 closely related Drosophila species (aged 300 Ky - 40 My) to identify new genes and characterize their molecular origin and evolution. Computational methods will be used to identify many new genes and map their origin (or loss) onto the known Drosophila phylogeny. Molecular and population genetics methods will then be used to validate function for a subset of these new genes from patterns of gene expression and from historical evidence for purifying and/or positive selection in patterns of DNA polymorphism and divergence. This work will provide a full portrait of the evolutionary origin of new genes and, importantly, contribute to the complete functional annotation of all the genomes surveyed. The methods developed will be applicable in comparative analysis of other genomes, including those of humans and their primate relatives. [unreadable] [unreadable]